.\" Automatically generated by Pod::Man 4.10 (Pod::Simple 3.35) .\" .\" Standard preamble: .\" ======================================================================== .de Sp \" Vertical space (when we can't use .PP) .if t .sp .5v .if n .sp .. .de Vb \" Begin verbatim text .ft CW .nf .ne \\$1 .. .de Ve \" End verbatim text .ft R .fi .. .\" Set up some character translations and predefined strings. \*(-- will .\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left .\" double quote, and \*(R" will give a right double quote. \*(C+ will .\" give a nicer C++. Capital omega is used to do unbreakable dashes and .\" therefore won't be available. \*(C` and \*(C' expand to `' in nroff, .\" nothing in troff, for use with C<>. .tr \(*W- .ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p' .ie n \{\ . ds -- \(*W- . ds PI pi . if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch . if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch . ds L" "" . ds R" "" . ds C` "" . ds C' "" 'br\} .el\{\ . ds -- \|\(em\| . ds PI \(*p . ds L" `` . ds R" '' . ds C` . ds C' 'br\} .\" .\" Escape single quotes in literal strings from groff's Unicode transform. .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" .\" If the F register is >0, we'll generate index entries on stderr for .\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index .\" entries marked with X<> in POD. Of course, you'll have to process the .\" output yourself in some meaningful fashion. .\" .\" Avoid warning from groff about undefined register 'F'. .de IX .. .nr rF 0 .if \n(.g .if rF .nr rF 1 .if (\n(rF:(\n(.g==0)) \{\ . if \nF \{\ . de IX . tm Index:\\$1\t\\n%\t"\\$2" .. . if !\nF==2 \{\ . nr % 0 . nr F 2 . \} . \} .\} .rr rF .\" ======================================================================== .\" .IX Title "Ace::Sequence::Multi 3pm" .TH Ace::Sequence::Multi 3pm "2018-11-01" "perl v5.28.0" "User Contributed Perl Documentation" .\" For nroff, turn off justification. Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" Ace::Sequence::Multi \- Combine Feature Tables from Multiple Databases .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 1 \& use Ace::Sequence::Multi; \& \& # open reference database \& $ref = Ace\->connect(\-host=>\*(Aqstein.cshl.org\*(Aq,\-port=>200009); \& \& # open some secondary databases \& $db1 = Ace\->connect(\-host=>\*(Aqstein.cshl.org\*(Aq,\-port=>200010); \& $db2 = Ace\->connect(\-path=>\*(Aq/usr/local/acedb/mydata\*(Aq); \& \& # Make an Ace::Sequence::Multi object \& $seq = Ace::Sequence::Multi\->new(\-name => \*(AqCHROMOSOME_I, \& \-db => $ref, \& \-offset => 3_000_000, \& \-length => 1_000_000); \& \& # add the secondary databases \& $seq\->add_secondary($db1,$db2); \& \& # get all the homologies (a list of Ace::Sequence::Feature objs) \& @homol = $seq\->features(\*(AqSimilarity\*(Aq); \& \& # Get information about the first one \-\- goes to the correct db \& $feature = $homol[0]; \& $type = $feature\->type; \& $subtype = $feature\->subtype; \& $start = $feature\->start; \& $end = $feature\->end; \& $score = $feature\->score; \& \& # Follow the target \& $target = $feature\->info; \& \& # print the target\*(Aqs start and end positions \& print $target\->start,\*(Aq\-\*(Aq,$target\->end, "\en"; .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" \&\fIAce::Sequence::Multi\fR transparently combines information stored about a sequence in a reference database with features tables from any number of annotation databases. The resulting object can be used just like an Ace::Sequence object, except that the features remember their database of origin and go back to that database for information. .PP This class will only work properly if the reference database and all annotation databases share the same cosmid map. .SH "OBJECT CREATION" .IX Header "OBJECT CREATION" You will use the \fBnew()\fR method to create new Ace::Sequence::Multi objects. The arguments are identical to the those in the Ace::Sequence parent class, with the addition of an option \&\fB\-secondary\fR argument, which points to one or more secondary databases from which to fetch annotation information. .IP "\-source" 4 .IX Item "-source" The sequence source. This must be an \fIAce::Object\fR of the \*(L"Sequence\*(R" class, or be a sequence-like object containing the SMap tag (see below). .IP "\-offset" 4 .IX Item "-offset" An offset from the beginning of the source sequence. The retrieved \&\fIAce::Sequence\fR will begin at this position. The offset can be any positive or negative integer. Offsets are \fB0\-based\fR. .IP "\-length" 4 .IX Item "-length" The length of the sequence to return. Either a positive or negative integer can be specified. If a negative length is given, the returned sequence will be complemented relative to the source sequence. .IP "\-refseq" 4 .IX Item "-refseq" The sequence to use to establish the coordinate system for the returned sequence. Normally the source sequence is used to establish the coordinate system, but this can be used to override that choice. You can provide either an \fIAce::Object\fR or just a sequence name for this argument. The source and reference sequences must share a common ancestor, but do not have to be directly related. An attempt to use a disjunct reference sequence, such as one on a different chromosome, will fail. .IP "\-name" 4 .IX Item "-name" As an alternative to using an \fIAce::Object\fR with the \fB\-source\fR argument, you may specify a source sequence using \fB\-name\fR and \fB\-db\fR. The \fIAce::Sequence\fR module will use the provided database accessor to fetch a Sequence object with the specified name. \fBnew()\fR will return undef is no Sequence by this name is known. .IP "\-db" 4 .IX Item "-db" This argument is required if the source sequence is specified by name rather than by object reference. It must be a previously opened handle to the reference database. .IP "\-secondary" 4 .IX Item "-secondary" This argument points to one or more previously-opened annotation databases. You may use a scalar if there is only one annotation database. Otherwise, use an array reference. You may add and delete annotation databases after the object is created by using the \&\fBadd_secondary()\fR and \fBdelete_secondary()\fR methods. .PP If \fBnew()\fR is successful, it will create an \fIAce::Sequence::Multi\fR object and return it. Otherwise it will return undef and return a descriptive message in Ace\->\fBerror()\fR. Certain programming errors, such as a failure to provide required arguments, cause a fatal error. .SH "OBJECT METHODS" .IX Header "OBJECT METHODS" Most methods are inherited from \fIAce::Sequence\fR. The following additional methods are supported: .IP "\fBsecondary()\fR" 4 .IX Item "secondary()" .Vb 1 \& @databases = $seq\->secondary; .Ve .Sp Return a list of the secondary databases currently in use, or an empty list if none. .IP "\fBadd_secondary()\fR" 4 .IX Item "add_secondary()" .Vb 1 \& $seq\->add_secondary($db1,$db2,...) .Ve .Sp Add one or more secondary databases to the list of annotation databases. Duplicate databases will be silently ignored. .IP "\fBdelete_secondary()\fR" 4 .IX Item "delete_secondary()" .Vb 1 \& $seq\->delete_secondary($db1,$db2,...) .Ve .Sp Delete one or more secondary databases from the list of annotation databases. Databases not already in use will be silently ignored. .SH "SEE ALSO" .IX Header "SEE ALSO" Ace, Ace::Object, Ace::Sequence,Ace::Sequence::Homol, Ace::Sequence::FeatureList, Ace::Sequence::Feature, \s-1GFF\s0 .SH "AUTHOR" .IX Header "AUTHOR" Lincoln Stein with extensive help from Jean Thierry-Mieg .PP Copyright (c) 1999, Lincoln D. Stein .PP This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See \s-1DISCLAIMER\s0.txt for disclaimers of warranty.